IMCA-CAT News

The Alio goniometer has a problem with one of the stages. The Y-axis is the affected axis which provides the raster centering at phi=0. - For automated operation, we do not recommend, and have never recommended, using the 5um or 10um aperture. - For automated operation, we suggest collecting a sweep from -90 to 90 to reduce the possibility of the sample rotating out of the beam. - For manual operation, we suggest taking test shots every 45 deg from phi=-90 to 180 to ensure the crystal will stay in the beam and then collecting an appropriate sweep. - Crystals less than 10um may be problematic, as may thin plates, however, we do recommend trying them anyway to see how they behave. - Symptoms of problems would be observing significant under- or overshoot of the expected position during centering, particularly at phi=0 or chronic rotation out of the beam during automated collection. - If significant problems occur, the staff can be asked to clean the stages which will usually, temporarily, improve their motion. - Repair of the stages is planned during the January 2017 shutdown.

JDirector 2.2.1_imca45.4 has been released. This update provides improvements and fixes to the instrument setup and auto-mode.

• The instrument setup (Instrument -> Setup... menu) will now update the Phi position if the "Initialize Goniometer" checkbox is checked. Previously, if the position was changed outside of JDirector and this setup was performed, the position would not be updated in JDirector.

• If an axis move timeout error is detected, an attempt to resync the positions of the XYZ stage and goniometer axes will be made. This can help avoid certain situations where JDirector and CameraMan think the axes are at different positions than they actually are.

• The Error Messages dialog now lists errors with a timestamp and in reverse chronological order so that the most recent error is at the top.

• A new built-in job sample step called VerifyMount has been added which attempts to verify that the mount was successful. In particular, an attempt is made to ensure that a robot collision did not occur during the mount. If a collision may have occurred, the job is aborted. This reduces the chance of a rogue robot job that destroys all the samples by mounting them on top of each other, one after the other, or by failing to mount them in some other way.

JDirector 2.2.1_imca44 has been released. This update provides improvements and fixes to the crystal view and diffraction centering.

• The Crystal View "Save Camera Image As..." pop-up menu item operation will now display an error message to the user if no suitable image writer was found based on the name of the destination file. Previously, an exception was thrown if the file had no extension, or, if no image writer was found for the extension, a zero-length file was written, and the user was not informed that no suitable writer was found.

• Increased the size of the manual diffraction center result history from 10 to 20. This is helpful for projects where there's a need to compare rasters when there might be multiple sites of interest or when regions might be rasterized again with a smaller cell size.

• Improved the diffraction center moves and syncs of the XYZ stage and Phi. In the auto-mode diffraction center, the move or sync of Phi was not interruptible, so if it hung, there was no way to stop it. This has been changed to be interruptible. In the manual-mode diffraction center, when the XYZ stage or Phi were moved or synced, it did not wait for those operations to complete. This has been corrected.

Subject: Imcadr 0.36.0 released Imcadr 0.36.0 has been released. This update introduces new features.

• Added support for fly-scanning. Instead of doing a step-scan for each row or column of a raster, support a fly-scan for each row or column to reduce the time it takes to rasterize a raster.

• Added support for computer cluster scoring. To speed up raster cell scoring, support scoring on a computer cluster.

• Added configuration file support. Support reading a system-wide, user, and command-line-specified configuration file. Remove the cluster-key and cluster-nodes command line options; these are now specified in the configuration file.

• Added imcadr(1) and imcadr.conf(5) man pages. Reduce the imcadr --help output to a simple usage message since the arguments are documented in imcadr(1).

An engineer from Dectris was here Dec 2 to examine the detector. In the course of their investigation, they swapped cables and circuit boards in the detector and have determined that the problem is with the module, but they are not certain what the problem is. Fortunately the issue is on the edge of the detector and is therefore a cosmetic issue and less a functional problem.

In the meantime, a dead pixel mask has been incorporated in the detector server to block out this region of the image, so no additional work needs to be done from the users standpoint for processing.

A final resolution to this problem is being determined.

If there are any questions/concerns, please contact the staff.

The failed module in the detector has been replaced. In the process of this repair, we have noticed some issues with a chip in a module at the bottom of the detector. A Dectris engineer will be on-site Dec 2 to address this issue, which they believe is due to a loose cable.

The following command can be used in autoPROC to mask out the bad chip:

autoPROC_XdsKeyword_UNTRUSTED_RECTANGLE="798 859 2429 2526"

or use the following line in your XDS.INP file:

UNTRUSTED_RECTANGLE=798 859 2429 2526

A module in the Pilatus failed after the completion of data collection Tuesday Nov 10 and the start of collection Wed Nov 11.

An example image is available here: https://www.imca.aps.anl.gov/~battaile/IMCA/dummy_0001.cbf

If you are using autoPROC, this is the command line option you need to use to mask out the bad module:

JDirector 2.2.1_imca43.1 has been released. This update fixes a usability issue in manual diffraction centering.

• Only allow the characters "a-zA-Z_.-" in manual diffraction center "raster images folder" path elements. This avoids cryptic diffraction center errors caused by the inability of the Dectris Pilatus camserver software to handle paths containing certain characters (e.g. the space character). (The set of characters the camserver software can handle is undocumented.)

Aaproc 0.4.0 has been released. This update includes the following changes:

• Add NumThreadsPerProcessJob configuration option to control the number of threads to use per dataset processing job. This enables more efficient use of the available computing resources.
• Add "autoPROC_CreateGpxPictures=no" to the autoPROC "process" invocation. This keeps processing fast even if autoPROC supports and defaults to the creation of pictures of diffraction and predictions.

JDirector 2.2.1_imca42 has been released. This update adds support for auto-mode diffraction-center polygon-shaped rasters.

• Added support for a polygon raster shape (instead of only a rectangular shape) in auto-mode diffraction centering. This makes diffraction centering faster by skipping raster cells that lie outside the crystal loop and hence do not need to be scanned.